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With the fast development of modern sciences, opinions that people think about the natural system are basically changing, that is to say, turning from ideal simplification to objective complexity. Universal logic puts forward the conceptions of general correlation and general self-correlation, which is used to describe the flexibility of correlation of objective things exactly, and establish the architecture of universal logic. This paper analyzes the principles of universal logic and the correlation of complex system, defines the conceptions of "whole correlation" and "local correlation", and sets up the reasoning model of complex system based on universal logic, moreover, illuminates the applied steps with an example on control system of welding process. The paper states: this reasoning model strongly integrates the natural intuition and operating feasibility, and it gives the implementation procedure of universal logic in engineering applied fields, especially the flexible control for complex system firstly.